Contacts of the strand formed by residues 358 - 364 (chain I) in PDB entry 5BRR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 358 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I PHE* 4.8 2.5 - + - -
237I ILE* 3.9 24.7 - - + -
238I ALA 3.5 15.7 - - - +
239I ALA* 3.6 16.2 - - + -
247I LEU* 3.4 15.5 - - - +
275I LEU* 4.7 3.8 - - + -
276I PRO* 4.2 13.7 - - + -
278I PHE* 3.9 19.3 - + - -
354I ILE* 3.5 23.3 - - + -
356I ARG 3.4 15.3 - - - -
357I PRO* 1.3 75.6 - - - +
359I LEU* 1.3 71.8 + - - +
360I PHE* 4.8 3.6 - - + -
376I VAL* 2.6 72.0 + - + -
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Residues in contact with LEU 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I PHE* 5.7 2.0 - - + -
221I TYR* 5.1 1.6 - - + -
238I ALA* 2.9 41.4 + - + +
247I LEU* 3.5 39.3 - - + +
250I LEU* 4.6 11.2 - - + -
251I THR* 3.8 18.2 - - + -
254I LEU* 3.6 36.3 - - + -
262I TRP* 6.1 0.4 - - + -
358I PHE* 1.3 83.1 - - - +
360I PHE* 1.3 66.0 + - - +
361I VAL* 5.6 0.2 - - + -
373I MET* 5.7 0.2 - - + -
374I GLY 2.8 22.4 - - - +
375I GLN* 4.1 2.7 - - - -
376I VAL 4.4 0.7 - - - +
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Residues in contact with PHE 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I VAL* 4.0 19.1 - - + -
235I MET* 3.9 34.5 - - + -
236I PHE 3.1 13.2 - - - +
237I ILE* 4.4 6.5 - - + -
238I ALA* 5.8 0.2 - - - -
278I PHE* 4.6 10.8 - + - -
326I ILE* 4.1 15.0 - - + -
358I PHE* 4.8 3.1 - + + -
359I LEU* 1.3 82.3 - - - +
361I VAL* 1.3 75.3 + - - +
362I VAL* 4.0 17.0 - - + -
372I PHE* 4.4 3.8 - - + -
373I MET* 3.3 25.0 - - - +
374I GLY* 3.1 45.7 + - - -
376I VAL* 4.2 22.2 - - + -
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Residues in contact with VAL 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I SER 3.8 0.3 - - - +
235I MET* 3.3 3.1 - - - +
236I PHE* 2.7 41.1 + - + +
254I LEU* 4.3 17.0 - - + -
259I ILE* 4.2 28.0 - - + -
262I TRP* 5.4 2.7 - - + -
359I LEU* 5.6 0.2 - - + -
360I PHE* 1.3 82.7 - - - +
362I VAL* 1.3 79.9 + - - +
363I ARG* 4.5 7.0 - - + +
370I VAL* 3.8 18.2 - - + -
372I PHE 3.3 9.9 - - - +
373I MET* 4.0 15.0 - - + -
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Residues in contact with VAL 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I PHE* 3.8 30.3 - - + -
228I TYR* 4.3 5.4 - - + -
233I LEU* 4.3 13.5 - - + -
234I SER 3.3 10.8 - - - +
235I MET* 3.7 26.7 - - + -
326I ILE* 5.2 0.2 - - + -
360I PHE* 4.0 5.8 - - + -
361I VAL* 1.3 86.2 - - - +
363I ARG* 1.3 62.1 + - - +
370I VAL* 3.8 1.2 - - - -
371I LEU* 3.1 24.8 + - + -
372I PHE* 3.0 40.4 + - + +
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Residues in contact with ARG 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I LEU* 3.2 30.4 - - - +
234I SER 2.9 12.1 + - - +
236I PHE* 3.5 35.6 - - + -
259I ILE* 3.7 18.4 - - + +
260I SER* 3.9 21.5 + - - +
263I LYS* 3.7 25.4 - - - +
361I VAL* 4.6 5.2 - - + -
362I VAL* 1.3 76.4 - - - +
364I HIS* 1.3 64.9 + - - +
365I ASN* 3.2 48.0 + - - +
368I GLY* 4.0 18.2 - - - +
369I THR 3.5 10.5 - - - +
370I VAL* 5.4 1.6 - - + -
371I LEU* 4.4 4.6 - - - +
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Residues in contact with HIS 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I LEU* 4.4 11.5 - - + +
81I GLU* 3.6 38.0 + - + +
82I LEU* 5.5 6.3 - - + -
86I TRP* 4.8 4.2 - + - -
232I THR* 3.8 8.1 - - + +
233I LEU* 3.8 19.5 - - + -
363I ARG* 1.3 74.0 - - - +
365I ASN* 1.3 51.4 + - - +
366I PRO* 3.2 22.4 - - + +
367I THR* 2.7 54.1 + - + +
368I GLY 2.8 27.5 + - - -
369I THR* 2.9 21.7 + - - +
371I LEU* 4.3 10.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il